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Nucleic Acids Research 2006 34(Database Issue):D511-D516; doi:10.1093/nar/gkj128
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Nucleic Acids Research, 2006, Vol. 34, Database issue D511-D516
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

MetaCyc: a multiorganism database of metabolic pathways and enzymes

Ron Caspi, Hartmut Foerster1, Carol A. Fulcher, Rebecca Hopkinson, John Ingraham2, Pallavi Kaipa, Markus Krummenacker, Suzanne Paley, John Pick, Seung Y. Rhee1, Christophe Tissier1, Peifen Zhang1 and Peter D. Karp*

SRI International 333 Ravenswood, Menlo Park, CA 94025, USA 1Department of Plant biology, Carnegie Institution 260 Panama Street, Stanford, CA 94305, USA 2Section of Microbiology, University of California Davis, One Shields Avenue, Davis, CA 95616, USA

*To whom correspondence should be addressed. Tel: +1 650 859 4358; Fax: +1 650 859 3735; Email: pkarp{at}ai.sri.com

Received September 15, 2005. Revised October 21, 2005. Accepted October 21, 2005.

MetaCyc is a database of metabolic pathways and enzymes located at http://MetaCyc.org/. Its goal is to serve as a metabolic encyclopedia, containing a collection of non-redundant pathways central to small molecule metabolism, which have been reported in the experimental literature. Most of the pathways in MetaCyc occur in microorganisms and plants, although animal pathways are also represented. MetaCyc contains metabolic pathways, enzymatic reactions, enzymes, chemical compounds, genes and review-level comments. Enzyme information includes substrate specificity, kinetic properties, activators, inhibitors, cofactor requirements and links to sequence and structure databases. Data are curated from the primary literature by curators with expertise in biochemistry and molecular biology. MetaCyc serves as a readily accessible comprehensive resource on microbial and plant pathways for genome analysis, basic research, education, metabolic engineering and systems biology. Querying, visualization and curation of the database is supported by SRI's Pathway Tools software. The PathoLogic component of Pathway Tools is used in conjunction with MetaCyc to predict the metabolic network of an organism from its annotated genome. SRI and the European Bioinformatics Institute employed this tool to create pathway/genome databases (PGDBs) for 165 organisms, available at the BioCyc.org website. These PGDBs also include predicted operons and pathway hole fillers.


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